Evolution Archives : Page 5 of 23 : Proslogion

No Doubt About It: These Proteins are From Dinosaurs

Fossil of a Brachylophosaurus at the Children's Museum of Indianapolis. (click for credit) — Fossil of a Brachylophosaurus at the Children’s Museum of Indianapolis. (click for credit)

In 2005, Dr. Mary Schweitzer shocked the paleontology community by reporting that she had found soft tissue in a Tyrannosaurus fossil that was thought to be 65 million years old. Since then, numerous other cases of soft tissue in dinosaur fossils have been reported (see here, here, here, here, and here, for example). Currently, the “record holder” for soft tissue is a worm fossil that is supposed to be 550 million years old!

While such discoveries have been met with skepticism, the overwhelming evidence points to the fact that there is soft tissue in many fossils that are supposed to be millions of years old. Of course, the next obvious issue to address is the chemical makeup of these soft tissues. Are the large biomolecules that we expect to find in soft tissue there? Are they intact or severely decayed? After all, most proteins are expected to decay significantly in as “little” as 30,000 years. Despite this fact, some of these fossils contain what appear to be intact proteins.

Now, of course, there is always the possibility of contamination. Fossil collection isn’t the cleanest of pursuits, and proteins are found pretty much everywhere on the planet. Thus, it is possible that the proteins which have been discovered in dinosaur bones aren’t really from the dinosaurs. However, two recent studies indicate that contamination cannot be the explanation. These proteins are real, and they really are from the dinosaurs themselves.

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Evolutionists Couldn’t Have Been More Wrong About Antibiotic Resistance

A colony of bacteria similar to the one analyzed in the study being discussed. (click for credit)

Back when I went to university, I was taught (as definitive fact) that bacteria evolved resistance to antibiotics as a result of the production of antibiotics. This was, of course, undeniable evidence for the fact that new genes can arise through a process of mutation and natural selection. Like most evolution-inspired ideas, however, the more we learned about antibiotic resistance in bacteria, the more we learned that there was a problem. It turns out that some cases of antibiotic resistance in bacteria were not caused by antibiotic-resistant genes. Instead, they were caused by the deterioration of genes that exist for other purposes. For example, the Anthrax bacterium can develop resistance to a class of antibiotics called quinolones, but it is the result of a mutation that degrades the gene that produces gyrase, the enzyme that those antibiotics attack. This allows the bacterium to survive the antibiotic, but the degraded gyrase gene causes the bacterium to reproduce much more slowly.

There are, however, specific genes found in bacteria that do produce proteins which fight antibiotics. It was generally thought that these genes arose through mutation and natural selection in response to our development of antibiotics. However, we now know that this just isn’t true. Antibiotic-resistant genes existed long before people developed antibiotics. I first wrote about this more than five years ago, when researchers found bacterial, antibiotic-resistant genes in permafrost alongside mammoth genes. Obviously, people weren’t making antibiotics when mammoths were alive. Thus, those genes existed long before human-made antibiotics. Later, I wrote about researchers who found bacterial, antibiotic-resistant genes in fossilized feces from the Middle Ages. Once again, this shows that antibiotic-resistant genes have been around long before our development of antibiotics.

Now an even more impressive study has been released. In it, researchers analyzed the DNA of a bacterium from the genus Paenibacillus. These bacteria form colonies, such as the one shown in the image above. The colors in the image indicate the density of bacteria – the brighter the yellow color, the higher the density of bacteria. While this genus of bacteria has been found in many, many environments, the specific species analyzed in the study was special: it has been living in a cave that has been isolated from the modern world. In fact, the cave is so isolated that no animals had ever ventured into it. When the researchers analyzed the DNA of this bacterium, they found all sorts of antibiotic-resistant genes.

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Confirmation of Feathers On A Dinosaur?

Image of a remarkable feathered fossil preserved in Amber. (from the paper being discussed)

At university, I was taught (as definitive fact) that the scales on reptiles slowly evolved into feathers. While you can still find this idea in popular literature, serious evolutionists no longer suggest it, because there is simply too much evidence to the contrary. Most evolutionists today suggest that feathers, scales, and hair all evolved from a common ancestral structure. I am sure that if serious scientists are still discussing flagellate-to-philosopher evolution in 50 years, there will be yet another idea of how these structures evolved.

Because evolutionists no longer think that feathers evolved from scales, the currently-fashionable thing to teach as definitive fact is that at least some (if not all) dinosaurs had feathers. The problem is that solid evidence to back up this “fact” has been sorely lacking. There are some dinosaur fossils that give hints of feathers, but there are alternate interpretations of what those hints mean. There are other fossils that clearly show feathers, but it’s not clear the fossils are of dinosaurs.

Now all that has changed, at least according to some sources, because of a recently-reported fossil. The remarkable specimen (pictured above) is part of a tail that has been encased in amber. The amber has preserved both the bones in the tail and the feathers that covered it, giving paleontologists a superb sample to analyze. While the results of the analysis are not conclusive, I do think that they add to the case that at least some dinosaurs had feathers.

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More Confirmation of a Creationist Prediction

The centromere is the point at which a chromosome and its duplicate attach during cellular reproduction. (click for credit) — The centromere is the point at which a chromosome and its duplicate attach during cellular reproduction.
(click for credit)

Uninformed people often say that creationism cannot make testable predictions. Since testable predictions are a necessary part of any scientific theory, these people claim that the creationist view isn’t scientific. Of course, nothing could be further from the truth! Creation scientists regularly make testable predictions, many of which have already been verified by further scientific research (see here, here, here, here, here, and here).

One of the more stunning examples of a confirmed creationist prediction is given by the nature of DNA. Since the 1970s, evolutionists have taught (as an indisputable fact) that the majority of the human genome is made up of useless stretches of nonsensical sequences which have been collectively referred to as “junk DNA.” However, in a Herculean study of human DNA, the ENCODE team demonstrated that a minimum of 80% is used by the cell and therefore should not be referred to as “junk.” One of the scientists on the team (Dr. John A. Stamatoyannopolous) stated:

I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance…

Actually, there were several scientists predicting this very result! Creationists have been doing so for years.^*

Well, now that we know the vast majority of the human genome is functional, some scientists have removed the evolutionary blinders from their eyes (at least when it comes to the nature of DNA) and have begun to look at regions of the DNA that scientists have been assuring us could not possibly have any function whatsoever. When they study such regions, they (not surprisingly) find that those regions do have a function, and it is often a very important one.

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Dr. James Tour Tells Us How Little We Know About the Origin of Life

James Tour is a giant in the field of organic chemistry.

A few days ago, a reader asked me to review an article by Dr. James Tour, as well as a video of a talk that he gave. I was initially hesitant to do so, because Dr. Tour is a giant in the field of organic chemistry. For example, he is the T. T. and W. F. Chao Professor of Chemistry at Rice University. For those who aren’t familiar with the academic structure of universities, only the most elite professors are appointed to a position that is named in honor of someone else. This is called an “endowed professorship,” and anyone who holds such a position is in the upper echelon of academia. He has won several awards for his outstanding research accomplishments, including being named by Thomson Reuters as one of the top ten chemists in the world in 2009. Not only is his research outstanding, but he is also an excellent teacher, having earned the George R. Brown Award for Superior Teaching at Rice University in both 2007 and 2012. What could I possibly add to the words of someone so knowledgeable and distinguished?

After reading the article, however, I do think I have something to offer. Because of the nature of what he is trying to discuss, his article is very, very technical. There were times, quite frankly, when my eyes glazed over a bit. I didn’t listen to a lot of the video (it seems to cover the same ground as the article), but it is also quite technical. For those who do not have the fortitude to make it through such a technical article or talk, I thought I could summarize it.

The “take home” message is straightforward: We have no idea how some of the most basic molecules necessary for life could have been produced by unguided processes. Why does Dr. Tour feel compelled to write a detailed article making a statement that, in my mind, is quite obvious? He explains:

Those who think scientists understand the issues of prebiotic chemistry are wholly misinformed. Nobody understands them. Maybe one day we will. But that day is far from today. It would be far more helpful (and hopeful) to expose students to the massive gaps in our understanding. They may find a firmer — and possibly a radically different — scientific theory. [Note that “prebiotic chemistry” refers to the chemistry that occurred on earth before life existed.]

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Watch Your Assumptions: They Can Lead To False Conclusions!

Poor assumptions can lead to myths instead of facts (image from shutterstock.com by Thinglass)

I am always on the lookout for experiences that can be turned into a “teachable moment.” Over the past two weeks, I have had two such experiences, so I thought I would write about them. The first one was a result of my article entitled Reflections on the Ark Encounter, which is a positive review of the latest attraction produced by Answers in Genesis. The day after it was published, I got a Facebook message from someone who had shared my post with a friend of hers. In reply, this friend asked if I was a “real” scientist. She assured him that I was and shared my Facebook page with him. She was rather taken aback when her friend sent her the following reply:

A mimeographed “PhD” from whatever fundamentalist “college” he sent his box tops to is not qualification to shine a real scientist’s shoes, let alone make claims about the natural world. Further, any parents who buy into this complete fiction, and indoctrinate their kids in this manner, are guilty of emotional and mental child abuse, and in my opinion should be prosecuted. I cant think of a better way to sabotage a child’s future in a modern, scientific and technological society.

This didn’t surprise me, of course. I am used to having my credentials questioned and being insulted because I don’t slavishly “toe the line” when it comes to today’s scientific consensus. That comes with the territory. Indeed, Dr. Dan Shechtman was asked to leave his research group because he dared to question the scientific consensus. Of course, the data eventually proved him to be correct and the scientific consensus to be wrong. However, that was until after being ridiculed as a “quasi-scientist” by one of the greatest chemists who has ever lived!

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A Really Undeniable Book, Written By a Real Scientist

A book that discusses some undeniable truths.

Dr. Douglas Axe is a very interesting scientist. He did his undergraduate work at the University of California, Berkeley and got his Ph.D. in chemical engineering from Caltech. His thesis was focused on molecular biology, which is why you find his scientific papers published in The Journal of Molecular Biology, PloS One, and Biochemistry. He is also a co-author on a paper that appeared in the Proceedings of the National Academy of Sciences of the United States of America. Currently, he is the director of the Biologic Institute, which is a research organization that encourages its scientists to do their research from an Intelligent Design point of view. He is also one of the authors of Science and Human Origins, a book that surveys the evidence for human evolution and concludes that humans cannot be the result of an unguided, neo-Darwinian process. I recently had the pleasure of reading his latest book, Undeniable: How Biology Confirms Our Intuition That Life Is Designed.

The first thing you might notice about the book is its main title, which is the same as the main title of an error-riddled book written by Bill Nye. While Nye likes to call himself “The Science Guy,” some of his behavior is decidedly anti-science (see here and here, for example), and his book makes it clear that he doesn’t try to understand some of the issues that he discusses publicly. Unlike Nye’s book, this book is written by a real scientist who actually does educate himself on the issue about which he is writing. Indeed, most of what he writes in this book is directly related to the scientific work he has published over the years.

Before getting into the meat of the book, I think that a personal story he shares is worth noting. While he was a graduate student at Caltech, one of his final exams asked which biological molecule was likely the first “living” molecule. In other words, the person writing the exam wanted the student to relate what was currently the most fashionable conjecture regarding the origin of life. Here is how he describes his answer and its result:

I decided to give the expected answer in full and then – for extra credit – to state why I found that answer unconvincing. I explained why, contrary to the consensus view, I didn’t think any molecule has what would be needed to start life. As shrewd at that seemed at the time, I learned when my exam was returned (with points deducted) that we students were expected to not only know current thinking in biology but also accept it without resistance. We were there as much to be acculturated as educated. (kindle version, Chapter 1, emphasis his)

That is so true. If you ever wonder why so many scientists resist new thinking in the origins debate, it’s because they have been taught to resist it! Fortunately, some scientists (like Dr. Axe) don’t don’t take that lesson to heart. Instead, they do what scientists should do: question the existing paradigm when the data speak against it.

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A Desperate Attempt to Solve an Intractable Problem

Artist's conception of a large asteroid hitting the earth (click for credit) — Artist’s conception of a large asteroid hitting the earth (click for credit)

One of the many problems associated with an ancient earth is the young, faint sun. In a nutshell, we think we understand the way a star produces energy, and based on this understanding, a star starts off dim and grows brighter over time. Based on what we know, then, the sun should have been about 25% dimmer 3.8 billion years ago, when most evolutionists think life first emerged on earth. However, if the sun really were 25% dimmer back then, the earth would be far too frigid to support life.

This problem has been recognized for more than 40 years now, and evolutionists have worked hard on it (see here and here), but a solution has remained elusive. However, a recent paper has proposed a possible solution, and I found it interesting, because it illustrates exactly how desperate evolutionists are to get rid of this intractable problem.

In essence, the paper says that the way to fix the problem is to have earth pummeled by very large (greater than 100 kilometers in diameter) asteroids. They are so large that the authors call them “planetesimals”:

Planetesimals exceeding 100 km in diameter pummeled the early Earth for hundreds of Myr, resulting in large volumes of melt produced both by immediate depressurization and by subsequent mantle convection driven by the impact.

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Another Creationist Prediction Confirmed

A cluster of the bacteria discussed in the article

Dr. Richard Lenski, an evolutionary biologist at Michigan State University, has been running a long-term experiment on evolution. Indeed, it has been named the LTEE (Long-Term Evolution Experiment). It started back in 1988 and is still running today. It has followed 12 populations of the bacterium Escherichia coli through more than 50,000 generations, examining how environmental stress changes the bacteria’s genetic and physiological characteristics. More than 6 years ago, I discussed how the project was confirming the creationist view of the genome, and it continues to do just that. In addition, it has inspired another experiment that specifically confirmed a creationist prediction while, at the same time, falsifying an evolutionary one.

To understand what has happened, we need to go back to 2008. In that year, the LTEE showed that even though Escherichia coli normally can’t make use of a chemical called citrate when oxygen is present, one of the their populations developed that ability after 31,500 generations of existence.¹ As a result, it was dubbed the “citrate plus” population. How did that happen? At the time, no one knew. However, evolutionists thought it was the result of some rare event or combination of events, exactly the kind upon which evolution depends. New Scientist put it this way:

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the “citrate-plus” trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

Lenski himself was bold enough to write:

So the bacteria in this simple flask-world have split into two lineages that coexist by exploiting their common environment in different ways. And one of the lineages makes its living by doing something brand-new, something that its ancestor could not do.

That sounds a lot like the origin of species to me. What do you think?

Not surprisingly, a recent experiment has shown that the evolutionary predictions of Lenski and New Scientist are wrong. At the same time, it demonstrated that the predictions of both intelligent design advocates and creationists were correct.

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People Can Compensate for Bad Genes!

In DNA, a gene is made up of exons and introns. The exons determine the protein that is made.

DNA is incredibly complex, so it’s really not surprising that the more we examine it, the more it challenges our notions of how it works. Consider, for example, genes. They make up less than 2% of human DNA, but they are important, because they tell the body what proteins to make and how to make them. At one time, evolutionary scientists actually thought that the vast majority of the rest of human DNA was useless junk. However, like most evolutionary ideas, that notion has been falsified by the data.

Despite the fact that they represent less than 2% of human DNA, genes are obviously important, because most of the chemical reactions that occur in our bodies are controlled by and depend on the proteins that genes specify. Because of the amazing design behind DNA, however, a single gene can actually produce many, many different proteins. This is because, as shown in the drawing above, a gene is actually constructed of introns and exons. The exons represent functional modules in the gene, and the introns separate those modules. When a gene is read, the exons can be grouped in many different ways, producing many different proteins. Because only the exons are used in the production of proteins, geneticists often study an organism’s exome, which is the collection of all the exons in a organism’s DNA.

When it comes to animals, studying how the exome affects overall health is difficult, but straightforward. Scientists can damage the gene of an animal and see what health consequences arise. This is referred to as a gene knockout, and it is an invaluable tool for learning what a gene does. For example, when the gene lovingly referred to as PRDM9 is knocked out of mice, they become sterile.¹ Thus, we know that the PRDM9 gene is essential for reproduction in mice.

When it comes to humans, it’s not ethical to do gene knockouts. However, you can study a population and find examples of people who have a natural mutation that has disabled a gene. By comparing that person’s health to similar people who have a working version of that gene, you can learn something about how the gene affects health. A recent study published in the journal Science did just that, and the reported results were surprising, to say the least!

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